← Back to search
2qaa

Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3

Method: X-RAY DIFFRACTION Dmax: 76.6 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Streptogrisin-B

OrganismNot specified

UniProt P00777

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 115–299 Not recorded SO4 SULFATE ION × 2 CL CHLORIDE ION × 4 TYR TYROSINE × 1 LEU LEUCINE × 1 EDO 1,2-ETHANEDIOL × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1 ACY ACETIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；10 mg/mL SGPB in 10 mM MgCl2 1.0 M Li2SO4, 0.1 M HEPES-NaOH pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.23 Å R-free 0.127
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 115–299 Not recorded SO4 SULFATE ION × 3 CL CHLORIDE ION × 6 TYR TYROSINE × 1 LEU LEUCINE × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 3 ACY ACETIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；10 mg/mL SGPB in 10 mM MgCl2 1.0 M Li2SO4, 0.1 M HEPES-NaOH pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.23 Å R-free 0.127
3 Protein homooligomer Homooligomer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain A； UniProt 115–299 Chain B； UniProt 115–299 Not recorded SO4 SULFATE ION × 60 CL CHLORIDE ION × 120 TYR TYROSINE × 24 LEU LEUCINE × 24 EDO 1,2-ETHANEDIOL × 48 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 12 GOL GLYCEROL × 48 ACY ACETIC ACID × 36 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；10 mg/mL SGPB in 10 mM MgCl2 1.0 M Li2SO4, 0.1 M HEPES-NaOH pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.23 Å R-free 0.127

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2QAA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CSO CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-ILE18I IN COMPLEX WITH SGPB Deposited 1999-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG 4000 sodium potassium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å
1CT0 CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-SER18I IN COMPLEX WITH SGPB Deposited 1999-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；PEG 4000 sodium potassium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.80 Å
1CT2 CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-THR18I IN COMPLEX WITH SGPB Deposited 1999-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；PEG 4000 sodium potassium phosphate , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.65 Å
1CT4 CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-VAL18I IN COMPLEX WITH SGPB Deposited 1999-08-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；PEG 4000 sodium potassium phosphate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å
1DS2 CRYSTAL STRUCTURE OF SGPB:OMTKY3-COO-LEU18I Deposited 2000-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；PEG 4000, sodium potassium phosphate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.70 Å
1SGD ASP 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5 Deposited 1999-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.4M SODIUM/POTASSIUM PHOSPHATE BUFFER AT PH 6.5
Resolution 1.80 Å
1SGE GLU 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5 Deposited 1999-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.4 M SODIUM/POTASSIUM PHOSPHATE buffer AT PH 6.5
Resolution 1.80 Å
1SGN ASN 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B Deposited 1999-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；2% PEG 6000, 50MM SODIUM/POTASSIUM PHOSPHATE BUFFER AT PH 6.5, pH 6.50
Resolution 1.80 Å
1SGP ALA 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B Deposited 1995-05-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.40 Å
1SGQ GLY 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B Deposited 1995-05-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1SGR LEU 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B Deposited 1995-05-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1SGY TYR 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5 Deposited 1999-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.4 M SODIUM/POTASSIUM PHOSPHATE buffer AT PH 6.5
Resolution 1.80 Å
2GKV Crystal structure of the SGPB:P14'-Ala32 OMTKY3-del(1-5) complex Deposited 2006-04-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.2M Na acetate trihydrate, 0.1M Tris-HCl pH 8.5, 26% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.70 Å R-free 0.248
2NU0 Molecular structures of the complexes of SGPB with OMTKY3 aromatic P1 variants Trp18I, His18I, Phe18I, and Tyr18I Deposited 2006-11-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa） Fragment：residues 115-299
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；PEG 4000, SODIUM POTASSIUM PHOSPHATE, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.95 Å
2NU1 Molecular structures of the complexes of SGPB with OMTKY3 aromatic P1 variants Trp18I, His18I, Phe18I and Tyr18I Deposited 2006-11-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa） Fragment：residues 115-299
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；PEG 4000, SODIUM POTASSIUM PHOSPHATE, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å
2NU2 Accommodation of positively-charged residues in a hydrophobic specificity pocket: Crystal structures of SGPB in complex with OMTKY3 variants Lys18I and Arg18I Deposited 2006-11-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa） Fragment：residues 115-299
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；PEG 4000, SODIUM POTASSIUM PHOSPHATE, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.65 Å
2NU3 Accommodation of positively-charged residues in a hydrophobic specificity pocket: Crystal structures of SGPB in complex with OMTKY3 variants Lys18I and Arg18I Deposited 2006-11-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa） Fragment：residues 115-299
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；PEG 4000, SODIUM POTASSIUM PHOSPHATE, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å
2NU4 Accommodation of positively-charged residues in a hydrophobic specificity pocket: Crystal structures of SGPB in complex with OMTKY3 variants Lys18I and Arg18I Deposited 2006-11-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa） Fragment：residues 115-299
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG 4000, SODIUM POTASSIUM PHOSPHATE at pH 7.1 24h before data collection, crystal was transferred to PEG4000, NaKHPO4 at pH 10.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.75 Å
2QA9 Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2 Deposited 2007-06-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 115–299（185 aa）
Not recorded CL CHLORIDE ION × 4 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；298 K；10 mg/mL SGPB in 10 mM MgCl2 0.7 M KH2PO4 pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.18 Å R-free 0.182
2QA9 Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2 Deposited 2007-06-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded CL CHLORIDE ION × 2 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；298 K；10 mg/mL SGPB in 10 mM MgCl2 0.7 M KH2PO4 pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.18 Å R-free 0.182
2SGD ASP 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 10.7 Deposited 1999-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 10.7；0.4M SODIUM/POTASSIUM PHOSPHATE BUFFER AT PH 10.7
Resolution 1.80 Å
2SGE GLU 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 10.7 Deposited 1999-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 10.7；0.4M SODIUM/POTASSIUM PHOSPHATE BUFFER AT PH 10.7
Resolution 1.80 Å
2SGF PHE 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B Deposited 1999-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.4 M SODIUM/POTASSIUM PHOSPHATE AT PH 6.5
Resolution 1.75 Å
2SGP PRO 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5 Deposited 1999-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.4 M SODIUM/POTASSIUM PHOSPHATE BUFFER AT PH 6.5, pH 6.50
Resolution 1.80 Å
2SGQ GLN 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5 Deposited 1999-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.4 M SODIUM/POTASSIUM PHOSPHATE buffer AT PH 6.5
Resolution 1.80 Å
3SGB STRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEASE B AND THE THIRD DOMAIN OF THE TURKEY OVOMUCOID INHIBITOR AT 1.8 ANGSTROMS RESOLUTION Deposited 1983-01-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
3SGQ GLN 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 10.7 Deposited 1999-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 10.7；0.4 M SODIUM/POTASSIUM PHOSPHATE buffer AT PH 10.7
Resolution 1.80 Å
4SGB STRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEINASE B AND POLYPEPTIDE CHYMOTRYPSIN INHIBITOR-1 FROM RUSSET BURBANK POTATO TUBERS AT 2.1 ANGSTROMS RESOLUTION Deposited 1989-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 115–299（185 aa）
Not recorded SO4 SULFATE ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å

27 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRTB_STRGR
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–185； UniProt 115–299 Author chain B； PDBConstruct 1–185； UniProt 115–299

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2qaa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2qaa
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2qaa
Deposition date deposition_date2007-06-14
Structure title titleCrystal structure of the second tetrahedral intermediates of SGPB at pH 7.3
Keywords keywordsCHYMOTRYPSIN-TYPE SERINE PEPTIDASE, SECOND TETRAHEDRAL INTERMEDIATES, SINGLE AMINO ACIDS, BETA BARRELS, ALPHA HELIX, Hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.74 Å
Radius of gyration Rg (electron density) rg_electron21.76 Å
Forward intensity I(0) i031851500.00
Molecular weight molecular_weight39517.0 kDa
Excluded volume excluded_volume47717 ų
Envelope volume envelope_volume54021 ų
Hydration-shell volume shell_volume21386 ų
Envelope diameter envelope_diameter78.8 Å
Shell Rg shell_rg27.62 Å
Envelope Rg envelope_rg21.93 Å
Shape Rg shape_rg21.70 Å
Total Rg total_rg22.58 Å
Total atoms total_atoms2746
Residues n_residues356
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax76.6 Å
Rg (real space) rg_real22.78 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real3.1850e+07
I(0) uncertainty (real space) i0_real_error4.0540e+05
Rg (reciprocal space) rg_reciprocal22.78 Å
I(0) (reciprocal space) i0_reciprocal31850000.0000
Solution quality estimate total_estimate0.8723
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.2 Å
Skewness Skewness skewness0.414
Kurtosis Kurtosis kurtosis-0.360
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7501000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.953
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (10)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2qaaa_
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.1 — Prokaryotic proteases
Domain ID domain_idd2qaab_
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.1 — Prokaryotic proteases

CATH v4.4 (4 domains)

Domain ID domain_id2qaaA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id2qaaA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id2qaaB01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id2qaaB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
▶

8. Citations (1)

▶

9. Files and Curves (10)